Follow the instructions here to download Mission Planner or APM Planner. Then follow the instructions here to connect your receiver to Pixhawk and perform RC calibration. Do not complete the setup wizard or any other mandatory calibrations besides radio and flight modes; if the setup wizard appears, close it and go directly to Radio Calibration.
No, the initial setup process has already been completed for you, and your Aero is ready to fly! When using Mission Planner or APM Planner, re-performing the calibrations on the initial setup screen, including the mandatory hardware configurations and setup wizard, can adversely affect the performance of your aircraft. After downloading Mission Planner or APM Planner, select the flight data or flight plan screens to get started planning missions and monitoring your Aero. Do not complete the setup wizard or perform any of the calibrations on the initial setup screen unless you are connecting an RC system.
No, you cannot fly the Aero without a transmitter turned on and connected to your plane. During an autonomous mission, the Aero will be controlled by the autopilot without input from the transmitter, but you should always keep the transmitter turned on and ready to use at any moment.